X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=1d2526fdca83114dcca76217917324d134bcc391;hb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;hp=9e703ceeb62c2d610776c7f245980de651ab28a1;hpb=3117b1c3109121dff476997d3c5db5b47a77729b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 9e703ce..1d2526f 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,38 +11,49 @@
  */
 
 #include "command.hpp"
-#include "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
+#include "filters.h"
+#include "mpi.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-	FilterSeqsCommand() {};
+	FilterSeqsCommand(string);
 	~FilterSeqsCommand() {};
 	int execute();	
+	void help();
 	
 private:
-	void doTrump();
-	void doSoft();
-	void doFilter();
-	
-	GlobalData* globaldata;
-	string filename, trump, filter;
+	struct linePair {
+		int start;
+		int num;
+		linePair(long int i, long int j) : start(i), num(j) {}
+	};
+	vector<linePair*> lines;
+	vector<int> processIDS;
+
+	string vertical, filter, fasta, hard, outputDir, filterFileName;
+	vector<string> fastafileNames;	
+	int alignmentLength, processors;
+	vector<int> bufferSizes;
+	vector<string> outputNames;
+
+	char trump;
+	bool abort;
+	float soft;
+	int numSeqs;
 	
-	ReadFasta* readFasta;
-	ReadNexus* readNexus;
-	ReadClustal* readClustal;
-	ReadPhylip* readPhylip;
+	string createFilter();
+	int filterSequences();
+	int createProcessesCreateFilter(Filters&, string);
+	int createProcessesRunFilter(string, string);
+	int driverCreateFilter(Filters&, string, linePair*);
+	int driverRunFilter(string, string, string, linePair*);	
+	int driverMPIRun(istringstream&, MPI_File&);
+	int MPICreateFilter(Filters&, string);	
+	int setLines(string);
+	int parseBuffer(string, vector<string>&);
 	
-	vector<bool> columnsToRemove;
-	SequenceDB* db;
-	double soft;
 };
 
-#endif
\ No newline at end of file
+#endif